Open Tree of Life @Evolution 2012

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Open Tree of Life talk given at 2012 Evolution meetings in Ottawa, Canada

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Open Tree of Life @Evolution 2012

  1. 1. A community-assembled, continually updated evolutionary history of all life Karen A. Cranston National Evolutionary Synthesis Center Duke University
  2. 2. opentreeoflife.orgKaren Cranston (NESCent) Laura Katz (Smith) Gordon Burleigh (Florida) Rick Ree (FMNH) Keith Crandall (GWU) Stephen Smith (Michigan) Karl Gude (MSU) Doug Soltis (Florida) David Hibbett (Clark) Tiffani Williams (TAMU) Mark Holder (Kansas) AVAToL: Assembling, Visualizing and Analysis of the Tree of Life
  3. 3. Phylogenypapers,1978;2008 12000" 10000"Numberofpaperspublished 8000" Rapid"increase"in"applica?ons"of" phylogeny,"beginning"in"early"1990s" 6000" 4000" 2000" 0" 1978" 979" 980"1981" 982" 983" 984"1985" 986"1987" 988" 989" 990"1991" 992" 993" 994"1995" 996"1997" 998" 999" 000"2001" 002" 003" 004"2005" 006"2007" 008" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 Year Source:"ISI"Web"of"Science"" graph from David Hillis
  4. 4. Where can I browse,search and download acomplete tree of life? You can’t. (Yet)
  5. 5. DATA AVAILABILITY Community norm to archive sequence data ~4% of all published phylogenetic trees
  6. 6. Year one goals1. Synthesize a complete draft tree of life from existing phylogenetic trees2. Publish this draft tree with: a. ability to add annotations and upload new data sets b. highlighted areas of conflict and links to source data c. utilities to download whole tree and subtrees
  7. 7. + taxonomies of living and extinct species+ digital phylogenetic data: Assembling the Tree of Life (and other) projects recent high-profile phylogenies ribosomal RNA trees for Bacteria and Archaea TreeBASE and Dryad trees Graph database holding thousands of input trees with millions of nodes
  8. 8. Dipsicales graphtaxonomy data (578 taxa) +Soltis et al APG III phylogeny (30 taxa)
  9. 9. Dipsicales graph Synthesized tree (favouring phylogenetic branches); contains all 578 taxa
  10. 10. Graph database holdingthousands of input trees with • filter / weight input trees millions of nodes • build synthetic trees • compare to alternate trees • input new data sets
  11. 11. AUTOMATIC UPDATING update trees with new sequence data detect and synthesize newly published trees
  12. 12. SMART GENERATION OF FIGURES FOR PUBLICATION • Semantic annotation layers • Collaborative editing EVOLUTION • Integrated submission of data and annotations to archives Weigmann et al. PNAS, 2011ig. 1. Combined molecular phylogenetic tree for Diptera. Partitioned ML analysis of combined taxon sets of tier 1 and tier 2 FLYTREE data samples (−lnL =
  13. 13. ?• Increasing availability of digital data associated with phylogeny publications• Makingsynthetic tree open to community annotation and data submission• Simple access to search and download the tree of life
  14. 14. ?• Open Science • project wiki: opentree.wikispaces.com • mailing list (opentreeoflife@googlegroups.com) • development board (trello.org/opentree)
  15. 15. • provide complete phylogenetic framework• link to biodiversity and systematics content
  16. 16. • provide complete phylogenetic framework • link to biodiversity and systematics content• API for downloading subtrees to analysis tools
  17. 17. • provide complete phylogenetic framework • link to biodiversity and systematics content• API for downloading subtrees to analysis tools• source / storage of underlying data
  18. 18. opentreeoflife.org• We’ve only just started (June 1)• Looking for input, feedback and participation: • join the mailing list • add publications to the Mendeley group • vote / comment on plans on the Trello boards • participate in virtual data curation sprint in August

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